Align glucose transporter, ATPase component (characterized)
to candidate WP_011384921.1 AMB_RS12790 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_000009985.1:WP_011384921.1 Length = 232 Score = 88.6 bits (218), Expect = 1e-22 Identities = 71/231 (30%), Positives = 118/231 (51%), Gaps = 16/231 (6%) Query: 11 GATPLVEMKDISISFGG----IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQ 66 G L E+ I+ FG + A+ V + L+PGEVVGLLG +G+GKSTL+ ++ + Sbjct: 3 GPQVLAELTGIAKHFGEGASRVDALRGVDLSLHPGEVVGLLGPSGSGKSTLLNIIGCVVE 62 Query: 67 MDAGEIRVNGDKV-----EITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPF 121 +AG + ++G V + R R I I+Q L L++ N+ + EL Sbjct: 63 PNAGRMVLDGVVVYDGAWTGGDLRRLRLDKIGFIFQFHNLLPFLNSRDNVAVVLELAGQ- 121 Query: 122 GLVDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPT 181 D +A ++++ L + + P LSGG+ Q VAIARA+ N ++++ DEPT Sbjct: 122 ---DPAAARRRAGELLDYLEVGARAEASP-GQLSGGEAQRVAIARALANNPRLILADEPT 177 Query: 182 AALGPHETQMVAE-LIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQL 231 AAL +V + LI+ + Q + ++ HD + + DR +++G L Sbjct: 178 AALDSQRAAIVMDLLIKVAREQNAAVLVVSHD-EKIYDRFDRMVRVRDGVL 227 Lambda K H 0.317 0.135 0.373 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 141 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 232 Length adjustment: 24 Effective length of query: 236 Effective length of database: 208 Effective search space: 49088 Effective search space used: 49088 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory